Multiple sequence alignment - TraesCS5D01G382200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G382200 chr5D 100.000 3465 0 0 1 3465 451975000 451971536 0.000000e+00 6399.0
1 TraesCS5D01G382200 chr5D 80.508 236 31 7 175 399 451967027 451966796 2.140000e-37 167.0
2 TraesCS5D01G382200 chr5D 88.571 105 8 3 1281 1385 464931345 464931445 1.310000e-24 124.0
3 TraesCS5D01G382200 chr5B 89.508 1830 121 36 616 2418 551802693 551800908 0.000000e+00 2250.0
4 TraesCS5D01G382200 chr5B 88.270 844 40 21 2469 3282 551800898 551800084 0.000000e+00 955.0
5 TraesCS5D01G382200 chr5B 88.344 326 18 7 181 495 551803235 551802919 1.170000e-99 374.0
6 TraesCS5D01G382200 chr5B 88.785 214 9 9 3085 3286 551768204 551767994 7.430000e-62 248.0
7 TraesCS5D01G382200 chr5B 87.671 219 13 6 3034 3247 551741005 551740796 3.460000e-60 243.0
8 TraesCS5D01G382200 chr5B 83.456 272 22 12 1753 2023 551804186 551803937 7.480000e-57 231.0
9 TraesCS5D01G382200 chr5B 91.667 144 12 0 2616 2759 551776939 551776796 2.110000e-47 200.0
10 TraesCS5D01G382200 chr5B 89.017 173 3 1 11 183 551803426 551803270 2.110000e-47 200.0
11 TraesCS5D01G382200 chr5B 80.000 205 26 11 280 480 551696541 551696348 1.680000e-28 137.0
12 TraesCS5D01G382200 chr5B 93.333 45 3 0 574 618 458055387 458055431 2.230000e-07 67.6
13 TraesCS5D01G382200 chr5A 89.641 753 45 14 1489 2226 570795659 570794925 0.000000e+00 928.0
14 TraesCS5D01G382200 chr5A 91.339 381 26 4 181 557 570796945 570796568 6.630000e-142 514.0
15 TraesCS5D01G382200 chr5A 90.090 333 28 3 2467 2795 570792355 570792024 8.890000e-116 427.0
16 TraesCS5D01G382200 chr5A 84.737 380 36 15 616 988 570796367 570796003 9.140000e-96 361.0
17 TraesCS5D01G382200 chr5A 91.282 195 11 2 3097 3286 570789726 570789533 9.540000e-66 261.0
18 TraesCS5D01G382200 chr5A 85.882 170 13 6 17 183 570797141 570796980 1.650000e-38 171.0
19 TraesCS5D01G382200 chr5A 80.583 206 21 13 2035 2226 570788441 570788241 1.300000e-29 141.0
20 TraesCS5D01G382200 chr5A 96.364 55 2 0 3057 3111 570789794 570789740 1.320000e-14 91.6
21 TraesCS5D01G382200 chr5A 98.039 51 1 0 1933 1983 570788509 570788459 4.760000e-14 89.8
22 TraesCS5D01G382200 chr5A 83.908 87 8 4 461 546 570786977 570786896 1.030000e-10 78.7
23 TraesCS5D01G382200 chr2A 90.000 110 9 2 3284 3392 216837907 216837799 1.300000e-29 141.0
24 TraesCS5D01G382200 chr7D 96.296 81 1 1 3385 3465 168790965 168791043 7.800000e-27 132.0
25 TraesCS5D01G382200 chr7D 84.466 103 14 2 1286 1387 616367767 616367868 2.200000e-17 100.0
26 TraesCS5D01G382200 chr2B 87.719 114 13 1 1281 1393 570063958 570064071 7.800000e-27 132.0
27 TraesCS5D01G382200 chr2B 86.486 111 12 3 3284 3392 585195718 585195827 6.080000e-23 119.0
28 TraesCS5D01G382200 chr2B 88.542 96 9 2 3371 3465 81756666 81756760 7.860000e-22 115.0
29 TraesCS5D01G382200 chr2D 89.423 104 10 1 3290 3392 198728723 198728620 2.810000e-26 130.0
30 TraesCS5D01G382200 chr2D 87.755 98 11 1 3288 3385 175607896 175607992 2.830000e-21 113.0
31 TraesCS5D01G382200 chr2D 87.500 96 8 3 1292 1387 304428864 304428955 1.320000e-19 108.0
32 TraesCS5D01G382200 chr7A 93.182 88 4 2 3378 3465 162899901 162899986 1.010000e-25 128.0
33 TraesCS5D01G382200 chr7A 90.909 44 4 0 574 617 213620141 213620098 3.730000e-05 60.2
34 TraesCS5D01G382200 chr3A 92.308 91 6 1 3375 3465 691376571 691376660 1.010000e-25 128.0
35 TraesCS5D01G382200 chr3A 92.222 90 6 1 3376 3465 507465305 507465217 3.630000e-25 126.0
36 TraesCS5D01G382200 chr3A 86.667 60 5 2 3333 3392 123303117 123303061 2.890000e-06 63.9
37 TraesCS5D01G382200 chr1A 88.785 107 8 4 1281 1387 482330028 482329926 1.010000e-25 128.0
38 TraesCS5D01G382200 chr1A 96.154 78 3 0 3388 3465 531509490 531509567 1.010000e-25 128.0
39 TraesCS5D01G382200 chr1A 85.577 104 11 4 1285 1387 385653382 385653282 4.730000e-19 106.0
40 TraesCS5D01G382200 chr6B 93.976 83 5 0 3383 3465 474771202 474771120 3.630000e-25 126.0
41 TraesCS5D01G382200 chr3B 89.583 96 9 1 1281 1375 386948409 386948314 1.690000e-23 121.0
42 TraesCS5D01G382200 chr3B 93.182 44 3 0 574 617 819742581 819742624 8.030000e-07 65.8
43 TraesCS5D01G382200 chr1D 90.217 92 7 2 3376 3465 427704720 427704629 6.080000e-23 119.0
44 TraesCS5D01G382200 chr1B 91.011 89 6 2 3378 3465 114090670 114090757 6.080000e-23 119.0
45 TraesCS5D01G382200 chr1B 90.909 44 4 0 574 617 561697801 561697758 3.730000e-05 60.2
46 TraesCS5D01G382200 chr6D 85.577 104 11 4 1285 1386 388955825 388955926 4.730000e-19 106.0
47 TraesCS5D01G382200 chr4A 95.000 40 2 0 574 613 527130698 527130737 2.890000e-06 63.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G382200 chr5D 451971536 451975000 3464 True 6399.00 6399 100.0000 1 3465 1 chr5D.!!$R2 3464
1 TraesCS5D01G382200 chr5B 551800084 551804186 4102 True 802.00 2250 87.7190 11 3282 5 chr5B.!!$R5 3271
2 TraesCS5D01G382200 chr5A 570786896 570797141 10245 True 306.31 928 89.1865 17 3286 10 chr5A.!!$R1 3269

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
997 1950 0.25589 TGGCCTTAGGTCATGGCTTC 59.744 55.0 0.0 0.0 44.97 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2760 6287 0.036765 TGGACTGGTGGCGATGTTAC 60.037 55.0 0.0 0.0 0.0 2.5 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 859 4.966787 TTTGGTGGGCTGGCGTCC 62.967 66.667 6.41 6.41 34.70 4.79
120 873 3.255379 GTCCGGCGCGAATCTGTC 61.255 66.667 12.10 0.00 0.00 3.51
197 990 4.327898 TGATAACGTTTAACATCTGCGTCC 59.672 41.667 5.91 0.00 34.56 4.79
277 1070 2.742372 GTGCATGGCCGTCTTCGT 60.742 61.111 0.00 0.00 35.01 3.85
351 1144 4.273969 TCGGTTGACGCAAAGATTAGTTTT 59.726 37.500 0.00 0.00 43.86 2.43
467 1262 2.342279 TCCTCGCGTGGACTTTGG 59.658 61.111 25.07 6.79 0.00 3.28
477 1272 1.798813 GTGGACTTTGGCGTGTTCTAG 59.201 52.381 0.00 0.00 0.00 2.43
504 1305 3.474570 GCTCTCCTGGCGACCCAT 61.475 66.667 0.00 0.00 41.21 4.00
507 1308 1.903877 CTCTCCTGGCGACCCATGTT 61.904 60.000 0.00 0.00 41.21 2.71
611 1412 4.579270 GACAAGTATTTTCGGTCGAAGG 57.421 45.455 5.93 0.00 35.38 3.46
631 1575 5.975988 AGGGAGTACATGGTAATCACATT 57.024 39.130 8.55 0.00 0.00 2.71
664 1608 2.744202 CAAATCTGCCGTAGAGCAAAGT 59.256 45.455 0.00 0.00 43.52 2.66
694 1638 7.634522 AGAGAAGAAAAAGACGAAGACAATTG 58.365 34.615 3.24 3.24 0.00 2.32
696 1640 7.410485 AGAAGAAAAAGACGAAGACAATTGAC 58.590 34.615 13.59 6.06 0.00 3.18
706 1650 4.036262 CGAAGACAATTGACTCCAAAACCA 59.964 41.667 13.59 0.00 35.67 3.67
722 1666 2.440539 ACCAGAGTAGCAACAAGACG 57.559 50.000 0.00 0.00 0.00 4.18
725 1669 2.288213 CCAGAGTAGCAACAAGACGACA 60.288 50.000 0.00 0.00 0.00 4.35
726 1670 3.381045 CAGAGTAGCAACAAGACGACAA 58.619 45.455 0.00 0.00 0.00 3.18
727 1671 3.426859 CAGAGTAGCAACAAGACGACAAG 59.573 47.826 0.00 0.00 0.00 3.16
728 1672 2.135933 AGTAGCAACAAGACGACAAGC 58.864 47.619 0.00 0.00 0.00 4.01
729 1673 2.135933 GTAGCAACAAGACGACAAGCT 58.864 47.619 0.00 0.00 34.84 3.74
732 1676 1.330521 GCAACAAGACGACAAGCTCAA 59.669 47.619 0.00 0.00 0.00 3.02
733 1677 2.600792 GCAACAAGACGACAAGCTCAAG 60.601 50.000 0.00 0.00 0.00 3.02
734 1678 1.871080 ACAAGACGACAAGCTCAAGG 58.129 50.000 0.00 0.00 0.00 3.61
735 1679 1.151668 CAAGACGACAAGCTCAAGGG 58.848 55.000 0.00 0.00 0.00 3.95
736 1680 1.048601 AAGACGACAAGCTCAAGGGA 58.951 50.000 0.00 0.00 0.00 4.20
737 1681 1.048601 AGACGACAAGCTCAAGGGAA 58.951 50.000 0.00 0.00 0.00 3.97
738 1682 1.625818 AGACGACAAGCTCAAGGGAAT 59.374 47.619 0.00 0.00 0.00 3.01
739 1683 2.039084 AGACGACAAGCTCAAGGGAATT 59.961 45.455 0.00 0.00 0.00 2.17
747 1691 6.012745 ACAAGCTCAAGGGAATTAATTGTCT 58.987 36.000 5.17 0.00 0.00 3.41
775 1720 5.178809 GGAAGAAGAAAGGAAATCGACGAAA 59.821 40.000 0.00 0.00 0.00 3.46
805 1750 7.099764 TCTTTTAGTCTCGAGCTCAAATGATT 58.900 34.615 15.40 5.21 0.00 2.57
997 1950 0.255890 TGGCCTTAGGTCATGGCTTC 59.744 55.000 0.00 0.00 44.97 3.86
998 1951 0.255890 GGCCTTAGGTCATGGCTTCA 59.744 55.000 0.00 0.00 44.97 3.02
1010 1963 3.694072 TCATGGCTTCAACCTTAAATCGG 59.306 43.478 0.00 0.00 0.00 4.18
1011 1964 1.816224 TGGCTTCAACCTTAAATCGGC 59.184 47.619 0.00 0.00 0.00 5.54
1012 1965 1.134367 GGCTTCAACCTTAAATCGGCC 59.866 52.381 0.00 0.00 0.00 6.13
1013 1966 1.202143 GCTTCAACCTTAAATCGGCCG 60.202 52.381 22.12 22.12 0.00 6.13
1014 1967 0.806241 TTCAACCTTAAATCGGCCGC 59.194 50.000 23.51 0.00 0.00 6.53
1015 1968 0.321741 TCAACCTTAAATCGGCCGCA 60.322 50.000 23.51 10.36 0.00 5.69
1016 1969 0.098728 CAACCTTAAATCGGCCGCAG 59.901 55.000 23.51 10.56 0.00 5.18
1019 1972 0.588252 CCTTAAATCGGCCGCAGATG 59.412 55.000 23.51 8.57 0.00 2.90
1020 1973 1.299541 CTTAAATCGGCCGCAGATGT 58.700 50.000 23.51 6.77 0.00 3.06
1021 1974 1.261619 CTTAAATCGGCCGCAGATGTC 59.738 52.381 23.51 0.00 0.00 3.06
1022 1975 0.464036 TAAATCGGCCGCAGATGTCT 59.536 50.000 23.51 0.74 0.00 3.41
1045 2082 1.135689 GTGGCTGCGATTTTACTGTGG 60.136 52.381 0.00 0.00 0.00 4.17
1047 2084 0.804989 GCTGCGATTTTACTGTGGCT 59.195 50.000 0.00 0.00 0.00 4.75
1062 2099 2.743664 TGTGGCTTCGATCAAATCACTG 59.256 45.455 0.00 0.00 0.00 3.66
1068 2105 3.198409 TCGATCAAATCACTGGATGGG 57.802 47.619 0.00 0.00 32.92 4.00
1133 2170 4.503714 TTCTCTTTTTGAGTGGAGTGGT 57.496 40.909 0.00 0.00 43.13 4.16
1150 2187 9.391006 GTGGAGTGGTACATTAGATTTTGATAA 57.609 33.333 0.00 0.00 44.52 1.75
1156 2193 8.178964 TGGTACATTAGATTTTGATAACAACGC 58.821 33.333 0.00 0.00 35.63 4.84
1174 2211 3.670625 ACGCTTGTAGGCATGAACTTTA 58.329 40.909 0.00 0.00 0.00 1.85
1205 2242 6.743575 ATTTCCTTCAAAATAGTGTCTCGG 57.256 37.500 0.00 0.00 0.00 4.63
1268 2305 5.062183 TCGCACAAATCTGAAGATTCTAACG 59.938 40.000 6.03 8.48 43.41 3.18
1284 2321 5.971895 TCTAACGTAACCAAGTTTGTCAC 57.028 39.130 0.00 0.00 0.00 3.67
1299 2336 0.745845 GTCACTAGGCGGTCTACGGA 60.746 60.000 0.00 0.00 44.51 4.69
1340 2378 1.578583 ACTGGTGTTCGTTGTACTGC 58.421 50.000 0.00 0.00 0.00 4.40
1341 2379 1.138266 ACTGGTGTTCGTTGTACTGCT 59.862 47.619 0.00 0.00 0.00 4.24
1348 2386 5.445939 GGTGTTCGTTGTACTGCTATGATTG 60.446 44.000 0.00 0.00 0.00 2.67
1351 2389 6.090763 TGTTCGTTGTACTGCTATGATTGAAG 59.909 38.462 0.00 0.00 0.00 3.02
1352 2390 5.109210 TCGTTGTACTGCTATGATTGAAGG 58.891 41.667 0.00 0.00 0.00 3.46
1365 2403 7.663081 GCTATGATTGAAGGTGAATAGATTGGA 59.337 37.037 0.00 0.00 0.00 3.53
1373 2411 9.312904 TGAAGGTGAATAGATTGGAAATTTTCT 57.687 29.630 8.93 0.00 0.00 2.52
1428 2466 2.602211 CAGCTCGTACAGAAAGCAGATG 59.398 50.000 8.63 0.00 38.51 2.90
1479 2517 1.340114 GGAAAAGAAGGCCACCGAGAT 60.340 52.381 5.01 0.00 0.00 2.75
1480 2518 1.740025 GAAAAGAAGGCCACCGAGATG 59.260 52.381 5.01 0.00 0.00 2.90
1484 2522 0.755686 GAAGGCCACCGAGATGAGAT 59.244 55.000 5.01 0.00 0.00 2.75
1525 2563 4.329256 GGTTAGCTGAAACACGGAAGATAC 59.671 45.833 0.00 0.00 0.00 2.24
1526 2564 2.607187 AGCTGAAACACGGAAGATACG 58.393 47.619 0.00 0.00 37.36 3.06
1527 2565 2.029290 AGCTGAAACACGGAAGATACGT 60.029 45.455 0.00 0.00 46.82 3.57
1528 2566 3.192001 AGCTGAAACACGGAAGATACGTA 59.808 43.478 0.00 0.00 43.58 3.57
1555 2596 0.402121 AAGAGGTCAGCCCAAGGAAC 59.598 55.000 0.00 0.00 34.66 3.62
1635 2680 2.049985 GTCCGATCGATCAGGCCG 60.050 66.667 24.40 11.01 0.00 6.13
1649 2694 2.272471 GCCGGGAAGGAAGGAAGG 59.728 66.667 2.18 0.00 45.00 3.46
2070 3132 2.866762 CGTAGTGGTAGTACCGTAGTCC 59.133 54.545 14.67 0.00 42.58 3.85
2122 3196 3.249080 GCTTCGAGCTTCGTAGTAGAGAT 59.751 47.826 11.55 0.00 39.10 2.75
2137 3211 5.767269 AGTAGAGATCAGATGCATTGTACG 58.233 41.667 0.00 0.00 0.00 3.67
2161 3241 3.217599 TCACTTACGTCAGCTTGCTAG 57.782 47.619 0.00 0.00 0.00 3.42
2162 3242 2.557056 TCACTTACGTCAGCTTGCTAGT 59.443 45.455 0.00 0.00 0.00 2.57
2163 3243 2.663602 CACTTACGTCAGCTTGCTAGTG 59.336 50.000 0.00 6.58 0.00 2.74
2164 3244 1.656095 CTTACGTCAGCTTGCTAGTGC 59.344 52.381 0.00 0.00 40.20 4.40
2165 3245 0.888619 TACGTCAGCTTGCTAGTGCT 59.111 50.000 0.00 0.00 40.54 4.40
2166 3246 0.888619 ACGTCAGCTTGCTAGTGCTA 59.111 50.000 6.69 0.00 37.81 3.49
2179 3259 3.369471 GCTAGTGCTACTGGTGAAATGGA 60.369 47.826 0.00 0.00 36.03 3.41
2185 3265 3.998341 GCTACTGGTGAAATGGAACGTTA 59.002 43.478 0.00 0.00 0.00 3.18
2188 3268 3.190535 ACTGGTGAAATGGAACGTTATGC 59.809 43.478 0.00 0.00 0.00 3.14
2215 3295 4.013050 GCTCCAAGAATTTTACTGGCTCT 58.987 43.478 0.00 0.00 0.00 4.09
2226 3306 0.674895 ACTGGCTCTGGTGCGAATTC 60.675 55.000 0.00 0.00 0.00 2.17
2269 5790 2.292292 CCAACGGCTTAATTAATCGGGG 59.708 50.000 18.72 16.10 0.00 5.73
2272 5793 2.946990 ACGGCTTAATTAATCGGGGTTG 59.053 45.455 18.72 0.99 0.00 3.77
2279 5800 4.799715 AATTAATCGGGGTTGGGTGATA 57.200 40.909 0.00 0.00 0.00 2.15
2296 5817 4.242475 GTGATAACGTGTCCAAGTGATGA 58.758 43.478 0.00 0.00 0.00 2.92
2306 5827 5.122396 GTGTCCAAGTGATGACCTTTCATAC 59.878 44.000 0.00 0.00 42.95 2.39
2311 5832 6.656693 CCAAGTGATGACCTTTCATACTTCTT 59.343 38.462 0.00 0.00 42.95 2.52
2431 5958 1.880027 GTCGATTTTGTCCCAGCTGTT 59.120 47.619 13.81 0.00 0.00 3.16
2432 5959 1.879380 TCGATTTTGTCCCAGCTGTTG 59.121 47.619 13.81 3.36 0.00 3.33
2434 5961 2.293122 CGATTTTGTCCCAGCTGTTGAA 59.707 45.455 13.81 0.00 0.00 2.69
2436 5963 4.559300 CGATTTTGTCCCAGCTGTTGAATT 60.559 41.667 13.81 0.00 0.00 2.17
2437 5964 5.335583 CGATTTTGTCCCAGCTGTTGAATTA 60.336 40.000 13.81 0.00 0.00 1.40
2438 5965 4.846779 TTTGTCCCAGCTGTTGAATTAC 57.153 40.909 13.81 0.63 0.00 1.89
2439 5966 2.790433 TGTCCCAGCTGTTGAATTACC 58.210 47.619 13.81 0.00 0.00 2.85
2440 5967 2.107378 TGTCCCAGCTGTTGAATTACCA 59.893 45.455 13.81 0.29 0.00 3.25
2441 5968 3.153919 GTCCCAGCTGTTGAATTACCAA 58.846 45.455 13.81 0.00 0.00 3.67
2442 5969 3.572255 GTCCCAGCTGTTGAATTACCAAA 59.428 43.478 13.81 0.00 0.00 3.28
2443 5970 4.038642 GTCCCAGCTGTTGAATTACCAAAA 59.961 41.667 13.81 0.00 0.00 2.44
2444 5971 4.837860 TCCCAGCTGTTGAATTACCAAAAT 59.162 37.500 13.81 0.00 0.00 1.82
2445 5972 5.047377 TCCCAGCTGTTGAATTACCAAAATC 60.047 40.000 13.81 0.00 0.00 2.17
2446 5973 5.047092 CCCAGCTGTTGAATTACCAAAATCT 60.047 40.000 13.81 0.00 0.00 2.40
2447 5974 6.152661 CCCAGCTGTTGAATTACCAAAATCTA 59.847 38.462 13.81 0.00 0.00 1.98
2448 5975 7.309744 CCCAGCTGTTGAATTACCAAAATCTAA 60.310 37.037 13.81 0.00 0.00 2.10
2449 5976 7.542130 CCAGCTGTTGAATTACCAAAATCTAAC 59.458 37.037 13.81 0.00 0.00 2.34
2450 5977 7.271223 CAGCTGTTGAATTACCAAAATCTAACG 59.729 37.037 5.25 0.00 0.00 3.18
2451 5978 6.526674 GCTGTTGAATTACCAAAATCTAACGG 59.473 38.462 0.00 0.00 0.00 4.44
2452 5979 6.383415 TGTTGAATTACCAAAATCTAACGGC 58.617 36.000 0.00 0.00 0.00 5.68
2453 5980 6.207810 TGTTGAATTACCAAAATCTAACGGCT 59.792 34.615 0.00 0.00 0.00 5.52
2454 5981 7.390996 TGTTGAATTACCAAAATCTAACGGCTA 59.609 33.333 0.00 0.00 0.00 3.93
2455 5982 8.403236 GTTGAATTACCAAAATCTAACGGCTAT 58.597 33.333 0.00 0.00 0.00 2.97
2456 5983 8.514330 TGAATTACCAAAATCTAACGGCTATT 57.486 30.769 0.00 0.00 0.00 1.73
2457 5984 8.962679 TGAATTACCAAAATCTAACGGCTATTT 58.037 29.630 0.00 0.00 0.00 1.40
2458 5985 9.797556 GAATTACCAAAATCTAACGGCTATTTT 57.202 29.630 0.00 0.00 34.09 1.82
2463 5990 9.984190 ACCAAAATCTAACGGCTATTTTAAAAA 57.016 25.926 4.44 0.00 32.89 1.94
2525 6052 3.551082 GTCTGACATGCTCATCTTCTTCG 59.449 47.826 2.24 0.00 0.00 3.79
2740 6267 2.150397 ACAGTCAGCAGAACCGTTAC 57.850 50.000 0.00 0.00 0.00 2.50
2750 6277 4.328983 AGCAGAACCGTTACGTTCATTATG 59.671 41.667 17.15 9.40 43.82 1.90
2759 6286 7.535940 ACCGTTACGTTCATTATGAAAATGTTG 59.464 33.333 9.39 0.00 38.22 3.33
2760 6287 7.007905 CCGTTACGTTCATTATGAAAATGTTGG 59.992 37.037 9.39 4.93 38.22 3.77
2778 6309 0.743345 GGTAACATCGCCACCAGTCC 60.743 60.000 0.00 0.00 32.32 3.85
2828 7413 2.154462 CAGTGGGTTCATCAGTTGACC 58.846 52.381 0.00 0.00 32.84 4.02
2846 7431 3.190744 TGACCTTGACGTGTTCTAGCTAG 59.809 47.826 15.01 15.01 0.00 3.42
2859 7452 4.615834 GCTAGCCGAGAGCCGTCG 62.616 72.222 2.29 0.00 45.47 5.12
2897 7490 1.644786 GGTCGCATGGGTTCTTTCCG 61.645 60.000 9.86 0.00 0.00 4.30
2916 7509 0.818938 GGTCGGAAGAGGAAGGACTC 59.181 60.000 0.00 0.00 43.49 3.36
2917 7510 0.818938 GTCGGAAGAGGAAGGACTCC 59.181 60.000 0.00 0.00 45.81 3.85
2941 7535 1.260206 CGAACCGAGAGATGTCAACG 58.740 55.000 0.00 0.00 0.00 4.10
2942 7536 1.401148 CGAACCGAGAGATGTCAACGT 60.401 52.381 8.17 0.00 0.00 3.99
2943 7537 1.986378 GAACCGAGAGATGTCAACGTG 59.014 52.381 0.00 3.83 0.00 4.49
2944 7538 1.244816 ACCGAGAGATGTCAACGTGA 58.755 50.000 0.00 0.00 0.00 4.35
2945 7539 1.611977 ACCGAGAGATGTCAACGTGAA 59.388 47.619 0.00 0.00 0.00 3.18
2946 7540 2.035449 ACCGAGAGATGTCAACGTGAAA 59.965 45.455 0.00 0.00 0.00 2.69
2947 7541 2.408704 CCGAGAGATGTCAACGTGAAAC 59.591 50.000 0.00 0.00 0.00 2.78
3018 7612 3.764434 AGATGTTCCAGAACTAGAAGCGA 59.236 43.478 11.56 0.00 41.67 4.93
3120 8651 7.621991 CACGAATTTTCACAGTGGAGTATATC 58.378 38.462 0.00 0.00 0.00 1.63
3127 8658 4.519350 TCACAGTGGAGTATATCTAAGCCG 59.481 45.833 0.00 0.00 0.00 5.52
3169 8700 6.475727 GCAAGTGCAGTATATATACATACGGG 59.524 42.308 22.00 14.84 41.59 5.28
3185 8724 0.723459 CGGGTTAAACAAAGCGCGTC 60.723 55.000 8.43 0.00 36.40 5.19
3207 8746 2.746362 ACTGCAATCTTAGTGCTTCTGC 59.254 45.455 0.86 0.00 42.69 4.26
3212 8751 4.855937 GCAATCTTAGTGCTTCTGCTTTTC 59.144 41.667 0.00 0.00 39.00 2.29
3226 8765 1.006832 CTTTTCCTATGTGGTCGGCG 58.993 55.000 0.00 0.00 37.07 6.46
3283 8827 3.503365 TGACGAATACCGGGGATAATCT 58.497 45.455 6.32 0.00 43.93 2.40
3286 8830 5.047802 TGACGAATACCGGGGATAATCTTAC 60.048 44.000 6.32 0.00 43.93 2.34
3287 8831 4.221482 ACGAATACCGGGGATAATCTTACC 59.779 45.833 6.32 0.00 43.93 2.85
3288 8832 4.221262 CGAATACCGGGGATAATCTTACCA 59.779 45.833 6.32 0.00 33.91 3.25
3289 8833 5.623824 CGAATACCGGGGATAATCTTACCAG 60.624 48.000 6.32 0.00 33.91 4.00
3290 8834 3.056201 ACCGGGGATAATCTTACCAGT 57.944 47.619 6.32 0.00 0.00 4.00
3291 8835 3.390819 ACCGGGGATAATCTTACCAGTT 58.609 45.455 6.32 0.00 0.00 3.16
3294 8838 4.578928 CCGGGGATAATCTTACCAGTTTTG 59.421 45.833 0.00 0.00 0.00 2.44
3297 8841 6.362248 GGGGATAATCTTACCAGTTTTGCTA 58.638 40.000 0.00 0.00 0.00 3.49
3298 8842 6.831868 GGGGATAATCTTACCAGTTTTGCTAA 59.168 38.462 0.00 0.00 0.00 3.09
3301 8845 8.613482 GGATAATCTTACCAGTTTTGCTAACTC 58.387 37.037 2.37 0.00 0.00 3.01
3305 8849 9.569122 AATCTTACCAGTTTTGCTAACTCTTAA 57.431 29.630 2.37 3.31 0.00 1.85
3306 8850 9.740710 ATCTTACCAGTTTTGCTAACTCTTAAT 57.259 29.630 2.37 0.00 0.00 1.40
3307 8851 9.216117 TCTTACCAGTTTTGCTAACTCTTAATC 57.784 33.333 2.37 0.00 0.00 1.75
3308 8852 6.481954 ACCAGTTTTGCTAACTCTTAATCG 57.518 37.500 2.37 0.00 0.00 3.34
3309 8853 6.228258 ACCAGTTTTGCTAACTCTTAATCGA 58.772 36.000 2.37 0.00 0.00 3.59
3310 8854 6.147328 ACCAGTTTTGCTAACTCTTAATCGAC 59.853 38.462 0.00 0.00 0.00 4.20
3311 8855 6.369065 CCAGTTTTGCTAACTCTTAATCGACT 59.631 38.462 0.00 0.00 0.00 4.18
3312 8856 7.230222 CAGTTTTGCTAACTCTTAATCGACTG 58.770 38.462 0.00 0.00 0.00 3.51
3314 8858 7.329717 AGTTTTGCTAACTCTTAATCGACTGAG 59.670 37.037 0.00 0.00 0.00 3.35
3315 8859 6.510879 TTGCTAACTCTTAATCGACTGAGA 57.489 37.500 11.16 1.02 0.00 3.27
3316 8860 5.881447 TGCTAACTCTTAATCGACTGAGAC 58.119 41.667 11.16 0.00 0.00 3.36
3317 8861 5.648526 TGCTAACTCTTAATCGACTGAGACT 59.351 40.000 11.16 0.00 0.00 3.24
3318 8862 6.151312 TGCTAACTCTTAATCGACTGAGACTT 59.849 38.462 11.16 0.81 0.00 3.01
3319 8863 7.030768 GCTAACTCTTAATCGACTGAGACTTT 58.969 38.462 11.16 0.00 0.00 2.66
3320 8864 7.008810 GCTAACTCTTAATCGACTGAGACTTTG 59.991 40.741 11.16 0.91 0.00 2.77
3321 8865 6.334102 ACTCTTAATCGACTGAGACTTTGT 57.666 37.500 11.16 0.00 0.00 2.83
3323 8867 7.883217 ACTCTTAATCGACTGAGACTTTGTTA 58.117 34.615 11.16 0.00 0.00 2.41
3331 8875 8.689251 TCGACTGAGACTTTGTTATATTTCAG 57.311 34.615 0.00 0.00 37.43 3.02
3332 8876 8.304596 TCGACTGAGACTTTGTTATATTTCAGT 58.695 33.333 3.71 3.71 44.64 3.41
3338 8882 7.910304 AGACTTTGTTATATTTCAGTCGATGC 58.090 34.615 0.00 0.00 0.00 3.91
3339 8883 7.766278 AGACTTTGTTATATTTCAGTCGATGCT 59.234 33.333 0.00 0.00 0.00 3.79
3341 8885 9.547753 ACTTTGTTATATTTCAGTCGATGCTAT 57.452 29.630 0.00 0.00 0.00 2.97
3358 8902 9.271828 TCGATGCTATATTTCTTTAATCTTGCA 57.728 29.630 0.00 0.00 36.25 4.08
3362 8906 9.353431 TGCTATATTTCTTTAATCTTGCATGGA 57.647 29.630 0.00 0.00 30.41 3.41
3363 8907 9.837525 GCTATATTTCTTTAATCTTGCATGGAG 57.162 33.333 0.00 0.00 0.00 3.86
3368 10309 6.609237 TCTTTAATCTTGCATGGAGATTCG 57.391 37.500 13.99 6.36 41.59 3.34
3371 10312 6.844696 TTAATCTTGCATGGAGATTCGTAC 57.155 37.500 13.99 0.00 41.59 3.67
3372 10313 3.885724 TCTTGCATGGAGATTCGTACA 57.114 42.857 0.00 0.00 0.00 2.90
3374 10315 3.056179 TCTTGCATGGAGATTCGTACACA 60.056 43.478 0.00 0.00 0.00 3.72
3381 10322 6.251376 GCATGGAGATTCGTACACAAATTTTC 59.749 38.462 0.00 0.00 0.00 2.29
3385 10326 8.073768 TGGAGATTCGTACACAAATTTTCTTTC 58.926 33.333 0.00 0.00 0.00 2.62
3386 10327 8.073768 GGAGATTCGTACACAAATTTTCTTTCA 58.926 33.333 0.00 0.00 0.00 2.69
3387 10328 9.107367 GAGATTCGTACACAAATTTTCTTTCAG 57.893 33.333 0.00 0.00 0.00 3.02
3405 10346 8.964476 TCTTTCAGTTTTGTTAGAACTCATCT 57.036 30.769 0.00 0.00 42.48 2.90
3410 10351 7.600375 TCAGTTTTGTTAGAACTCATCTAGCTG 59.400 37.037 0.00 0.00 41.59 4.24
3411 10352 7.600375 CAGTTTTGTTAGAACTCATCTAGCTGA 59.400 37.037 0.00 0.00 41.59 4.26
3412 10353 7.816995 AGTTTTGTTAGAACTCATCTAGCTGAG 59.183 37.037 19.62 19.62 46.59 3.35
3425 10366 9.243637 CTCATCTAGCTGAGTTTTAGTTATGTC 57.756 37.037 14.26 0.00 38.27 3.06
3427 10368 9.243637 CATCTAGCTGAGTTTTAGTTATGTCTC 57.756 37.037 0.00 0.00 0.00 3.36
3429 10370 8.972127 TCTAGCTGAGTTTTAGTTATGTCTCAT 58.028 33.333 0.00 0.00 32.73 2.90
3430 10371 9.593134 CTAGCTGAGTTTTAGTTATGTCTCATT 57.407 33.333 0.00 0.00 32.73 2.57
3431 10372 8.485976 AGCTGAGTTTTAGTTATGTCTCATTC 57.514 34.615 0.00 0.00 32.73 2.67
3432 10373 8.097038 AGCTGAGTTTTAGTTATGTCTCATTCA 58.903 33.333 0.00 0.00 32.73 2.57
3433 10374 8.171840 GCTGAGTTTTAGTTATGTCTCATTCAC 58.828 37.037 0.00 0.00 32.73 3.18
3443 10384 9.331282 AGTTATGTCTCATTCACTTTTATAGCC 57.669 33.333 0.00 0.00 0.00 3.93
3444 10385 9.109393 GTTATGTCTCATTCACTTTTATAGCCA 57.891 33.333 0.00 0.00 0.00 4.75
3445 10386 9.851686 TTATGTCTCATTCACTTTTATAGCCAT 57.148 29.630 0.00 0.00 0.00 4.40
3447 10388 7.988737 TGTCTCATTCACTTTTATAGCCATTG 58.011 34.615 0.00 0.00 0.00 2.82
3455 10396 7.062322 TCACTTTTATAGCCATTGGATGTGAT 58.938 34.615 6.95 0.00 0.00 3.06
3456 10397 7.013559 TCACTTTTATAGCCATTGGATGTGATG 59.986 37.037 6.95 0.00 0.00 3.07
3457 10398 5.710513 TTTATAGCCATTGGATGTGATGC 57.289 39.130 6.95 0.00 0.00 3.91
3458 10399 3.520691 ATAGCCATTGGATGTGATGCT 57.479 42.857 6.95 0.00 0.00 3.79
3459 10400 4.645863 ATAGCCATTGGATGTGATGCTA 57.354 40.909 6.95 0.00 0.00 3.49
3460 10401 3.520691 AGCCATTGGATGTGATGCTAT 57.479 42.857 6.95 0.00 0.00 2.97
3461 10402 4.645863 AGCCATTGGATGTGATGCTATA 57.354 40.909 6.95 0.00 0.00 1.31
3463 10404 5.008331 AGCCATTGGATGTGATGCTATAAG 58.992 41.667 6.95 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.342862 AGTGAAGGCGTAATATGCATCT 57.657 40.909 0.19 0.00 0.00 2.90
3 4 5.018539 AGTAAGTGAAGGCGTAATATGCA 57.981 39.130 6.81 0.00 0.00 3.96
5 6 5.236478 CCCAAGTAAGTGAAGGCGTAATATG 59.764 44.000 0.00 0.00 0.00 1.78
6 7 5.365619 CCCAAGTAAGTGAAGGCGTAATAT 58.634 41.667 0.00 0.00 0.00 1.28
7 8 4.761975 CCCAAGTAAGTGAAGGCGTAATA 58.238 43.478 0.00 0.00 0.00 0.98
9 10 2.872842 GCCCAAGTAAGTGAAGGCGTAA 60.873 50.000 0.00 0.00 0.00 3.18
10 11 1.338389 GCCCAAGTAAGTGAAGGCGTA 60.338 52.381 0.00 0.00 0.00 4.42
11 12 0.605589 GCCCAAGTAAGTGAAGGCGT 60.606 55.000 0.00 0.00 0.00 5.68
12 13 0.605319 TGCCCAAGTAAGTGAAGGCG 60.605 55.000 0.00 0.00 43.46 5.52
14 15 1.156736 CGTGCCCAAGTAAGTGAAGG 58.843 55.000 0.00 0.00 0.00 3.46
15 16 1.878953 ACGTGCCCAAGTAAGTGAAG 58.121 50.000 0.00 0.00 0.00 3.02
110 863 4.210304 GCGCCGTGACAGATTCGC 62.210 66.667 0.00 0.00 35.82 4.70
113 866 1.079197 TGATGCGCCGTGACAGATT 60.079 52.632 4.18 0.00 0.00 2.40
277 1070 2.186903 GCATCGAAGCCCCGAGAA 59.813 61.111 0.00 0.00 42.21 2.87
351 1144 4.100344 TCGCTAATAATACTCAGCCAACCA 59.900 41.667 0.00 0.00 0.00 3.67
427 1222 5.195940 ACTACTATTTGGTACGTGCTCCTA 58.804 41.667 3.01 0.00 0.00 2.94
433 1228 4.595116 CGAGGACTACTATTTGGTACGTG 58.405 47.826 0.00 0.00 0.00 4.49
467 1262 1.597445 CGTAGCCTAGCTAGAACACGC 60.597 57.143 22.70 15.64 42.11 5.34
500 1301 3.788937 GAAAGAATCCATGCAACATGGG 58.211 45.455 22.91 7.92 39.60 4.00
591 1392 3.007182 TCCCTTCGACCGAAAATACTTGT 59.993 43.478 6.32 0.00 33.34 3.16
592 1393 3.592059 TCCCTTCGACCGAAAATACTTG 58.408 45.455 6.32 0.00 33.34 3.16
593 1394 3.260128 ACTCCCTTCGACCGAAAATACTT 59.740 43.478 6.32 0.00 33.34 2.24
596 1397 3.763360 TGTACTCCCTTCGACCGAAAATA 59.237 43.478 6.32 0.00 33.34 1.40
597 1398 2.564062 TGTACTCCCTTCGACCGAAAAT 59.436 45.455 6.32 0.00 33.34 1.82
598 1399 1.962807 TGTACTCCCTTCGACCGAAAA 59.037 47.619 6.32 0.00 33.34 2.29
599 1400 1.619654 TGTACTCCCTTCGACCGAAA 58.380 50.000 6.32 0.00 33.34 3.46
602 1403 0.102481 CCATGTACTCCCTTCGACCG 59.898 60.000 0.00 0.00 0.00 4.79
603 1404 1.192428 ACCATGTACTCCCTTCGACC 58.808 55.000 0.00 0.00 0.00 4.79
604 1405 4.098960 TGATTACCATGTACTCCCTTCGAC 59.901 45.833 0.00 0.00 0.00 4.20
605 1406 4.098960 GTGATTACCATGTACTCCCTTCGA 59.901 45.833 0.00 0.00 0.00 3.71
606 1407 4.142026 TGTGATTACCATGTACTCCCTTCG 60.142 45.833 0.00 0.00 0.00 3.79
607 1408 5.353394 TGTGATTACCATGTACTCCCTTC 57.647 43.478 0.00 0.00 0.00 3.46
608 1409 5.975988 ATGTGATTACCATGTACTCCCTT 57.024 39.130 0.00 0.00 0.00 3.95
609 1410 5.667626 AGAATGTGATTACCATGTACTCCCT 59.332 40.000 0.00 0.00 0.00 4.20
611 1412 6.582636 TCAGAATGTGATTACCATGTACTCC 58.417 40.000 0.00 0.00 37.40 3.85
631 1575 4.191544 CGGCAGATTTGGACTTAATCAGA 58.808 43.478 0.00 0.00 35.04 3.27
664 1608 8.195436 TGTCTTCGTCTTTTTCTTCTCTCTTTA 58.805 33.333 0.00 0.00 0.00 1.85
694 1638 3.402628 TGCTACTCTGGTTTTGGAGTC 57.597 47.619 0.00 0.00 42.06 3.36
696 1640 3.476552 TGTTGCTACTCTGGTTTTGGAG 58.523 45.455 0.00 0.00 35.86 3.86
706 1650 3.643763 CTTGTCGTCTTGTTGCTACTCT 58.356 45.455 0.00 0.00 0.00 3.24
722 1666 6.151817 AGACAATTAATTCCCTTGAGCTTGTC 59.848 38.462 0.00 0.00 39.93 3.18
725 1669 6.603599 GGTAGACAATTAATTCCCTTGAGCTT 59.396 38.462 0.00 0.00 0.00 3.74
726 1670 6.122964 GGTAGACAATTAATTCCCTTGAGCT 58.877 40.000 0.00 0.00 0.00 4.09
727 1671 5.007724 CGGTAGACAATTAATTCCCTTGAGC 59.992 44.000 0.00 0.00 0.00 4.26
728 1672 5.527582 CCGGTAGACAATTAATTCCCTTGAG 59.472 44.000 0.00 0.00 0.00 3.02
729 1673 5.190132 TCCGGTAGACAATTAATTCCCTTGA 59.810 40.000 0.00 0.00 0.00 3.02
732 1676 5.427481 TCTTCCGGTAGACAATTAATTCCCT 59.573 40.000 6.70 1.31 0.00 4.20
733 1677 5.677567 TCTTCCGGTAGACAATTAATTCCC 58.322 41.667 6.70 0.00 0.00 3.97
734 1678 7.046033 TCTTCTTCCGGTAGACAATTAATTCC 58.954 38.462 10.73 0.00 0.00 3.01
735 1679 8.488651 TTCTTCTTCCGGTAGACAATTAATTC 57.511 34.615 10.73 0.00 0.00 2.17
736 1680 8.857694 TTTCTTCTTCCGGTAGACAATTAATT 57.142 30.769 10.73 0.00 0.00 1.40
737 1681 7.553044 CCTTTCTTCTTCCGGTAGACAATTAAT 59.447 37.037 10.73 0.00 0.00 1.40
738 1682 6.877322 CCTTTCTTCTTCCGGTAGACAATTAA 59.123 38.462 10.73 1.08 0.00 1.40
739 1683 6.211986 TCCTTTCTTCTTCCGGTAGACAATTA 59.788 38.462 10.73 0.00 0.00 1.40
747 1691 4.221262 TCGATTTCCTTTCTTCTTCCGGTA 59.779 41.667 0.00 0.00 0.00 4.02
775 1720 5.247084 TGAGCTCGAGACTAAAAGAGTACT 58.753 41.667 18.75 0.00 39.06 2.73
784 1729 5.111989 CCAATCATTTGAGCTCGAGACTAA 58.888 41.667 18.75 12.33 34.60 2.24
882 1829 8.903820 GGGCACATAATCTAGATTACTTTTGTT 58.096 33.333 24.17 6.95 36.24 2.83
891 1838 3.071602 AGCACGGGCACATAATCTAGATT 59.928 43.478 21.28 21.28 44.61 2.40
896 1843 0.464373 CCAGCACGGGCACATAATCT 60.464 55.000 14.57 0.00 44.61 2.40
971 1919 2.033602 ACCTAAGGCCAACCGCAC 59.966 61.111 5.01 0.00 42.76 5.34
997 1950 0.098728 CTGCGGCCGATTTAAGGTTG 59.901 55.000 33.48 0.00 0.00 3.77
998 1951 0.035820 TCTGCGGCCGATTTAAGGTT 60.036 50.000 33.48 0.00 0.00 3.50
1010 1963 1.812922 CCACTGAGACATCTGCGGC 60.813 63.158 0.00 0.00 0.00 6.53
1011 1964 1.812922 GCCACTGAGACATCTGCGG 60.813 63.158 0.00 0.00 31.59 5.69
1012 1965 1.082679 CAGCCACTGAGACATCTGCG 61.083 60.000 0.00 0.00 32.44 5.18
1013 1966 1.367599 GCAGCCACTGAGACATCTGC 61.368 60.000 0.00 0.00 39.82 4.26
1014 1967 1.082679 CGCAGCCACTGAGACATCTG 61.083 60.000 0.00 0.00 33.20 2.90
1015 1968 1.217511 CGCAGCCACTGAGACATCT 59.782 57.895 0.00 0.00 33.20 2.90
1016 1969 0.179089 ATCGCAGCCACTGAGACATC 60.179 55.000 3.09 0.00 42.43 3.06
1019 1972 1.160137 AAAATCGCAGCCACTGAGAC 58.840 50.000 3.09 0.00 42.43 3.36
1020 1973 2.028112 AGTAAAATCGCAGCCACTGAGA 60.028 45.455 3.51 3.51 43.61 3.27
1021 1974 2.094894 CAGTAAAATCGCAGCCACTGAG 59.905 50.000 0.00 0.00 36.37 3.35
1022 1975 2.076100 CAGTAAAATCGCAGCCACTGA 58.924 47.619 0.00 0.00 36.37 3.41
1045 2082 3.003068 CCATCCAGTGATTTGATCGAAGC 59.997 47.826 3.87 3.87 0.00 3.86
1047 2084 3.199727 TCCCATCCAGTGATTTGATCGAA 59.800 43.478 0.00 0.00 0.00 3.71
1062 2099 9.317936 GTTTGAATCATTAGATTTTTCCCATCC 57.682 33.333 0.00 0.00 44.30 3.51
1115 2152 4.764050 TGTACCACTCCACTCAAAAAGA 57.236 40.909 0.00 0.00 0.00 2.52
1116 2153 6.934645 TCTAATGTACCACTCCACTCAAAAAG 59.065 38.462 0.00 0.00 0.00 2.27
1117 2154 6.833041 TCTAATGTACCACTCCACTCAAAAA 58.167 36.000 0.00 0.00 0.00 1.94
1124 2161 7.865706 ATCAAAATCTAATGTACCACTCCAC 57.134 36.000 0.00 0.00 0.00 4.02
1133 2170 9.767684 CAAGCGTTGTTATCAAAATCTAATGTA 57.232 29.630 0.00 0.00 35.20 2.29
1205 2242 2.785540 TTTCCCCGTATGGTTGGTAC 57.214 50.000 0.00 0.00 0.00 3.34
1232 2269 3.840890 TTTGTGCGAGTGTTGTTTTCT 57.159 38.095 0.00 0.00 0.00 2.52
1284 2321 0.875728 CAGATCCGTAGACCGCCTAG 59.124 60.000 0.00 0.00 34.38 3.02
1340 2378 9.565090 TTCCAATCTATTCACCTTCAATCATAG 57.435 33.333 0.00 0.00 0.00 2.23
1341 2379 9.919416 TTTCCAATCTATTCACCTTCAATCATA 57.081 29.630 0.00 0.00 0.00 2.15
1348 2386 9.794685 GAGAAAATTTCCAATCTATTCACCTTC 57.205 33.333 1.57 0.00 0.00 3.46
1351 2389 7.698130 CACGAGAAAATTTCCAATCTATTCACC 59.302 37.037 1.57 0.00 0.00 4.02
1352 2390 8.450964 TCACGAGAAAATTTCCAATCTATTCAC 58.549 33.333 1.57 0.00 0.00 3.18
1443 2481 2.760385 CCGTGTCTCCCCTCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
1446 2484 0.977395 CTTTTCCGTGTCTCCCCTCT 59.023 55.000 0.00 0.00 0.00 3.69
1479 2517 0.609151 TTAACGAACGGGCCATCTCA 59.391 50.000 4.39 0.00 0.00 3.27
1480 2518 1.949465 ATTAACGAACGGGCCATCTC 58.051 50.000 4.39 0.00 0.00 2.75
1484 2522 0.882474 CCAAATTAACGAACGGGCCA 59.118 50.000 4.39 0.00 0.00 5.36
1525 2563 3.678548 GGCTGACCTCTTTTTGTAGTACG 59.321 47.826 0.00 0.00 0.00 3.67
1526 2564 4.001652 GGGCTGACCTCTTTTTGTAGTAC 58.998 47.826 0.00 0.00 35.85 2.73
1527 2565 3.649023 TGGGCTGACCTCTTTTTGTAGTA 59.351 43.478 0.00 0.00 41.11 1.82
1528 2566 2.441750 TGGGCTGACCTCTTTTTGTAGT 59.558 45.455 0.00 0.00 41.11 2.73
1555 2596 0.250513 CCTCTTCCGGTCTTCCCTTG 59.749 60.000 0.00 0.00 0.00 3.61
1620 2665 4.363990 CCCGGCCTGATCGATCGG 62.364 72.222 24.71 24.71 40.32 4.18
1635 2680 1.492599 CTCATCCCTTCCTTCCTTCCC 59.507 57.143 0.00 0.00 0.00 3.97
1649 2694 4.962836 CCATGGCGGGGCTCATCC 62.963 72.222 0.00 0.00 0.00 3.51
1699 2751 3.188786 GACGATGAGCACCGCCAC 61.189 66.667 0.00 0.00 0.00 5.01
2122 3196 2.279741 GAAGGCGTACAATGCATCTGA 58.720 47.619 0.00 0.00 0.00 3.27
2161 3241 2.159627 CGTTCCATTTCACCAGTAGCAC 59.840 50.000 0.00 0.00 0.00 4.40
2162 3242 2.224426 ACGTTCCATTTCACCAGTAGCA 60.224 45.455 0.00 0.00 0.00 3.49
2163 3243 2.423577 ACGTTCCATTTCACCAGTAGC 58.576 47.619 0.00 0.00 0.00 3.58
2164 3244 5.447279 GCATAACGTTCCATTTCACCAGTAG 60.447 44.000 2.82 0.00 0.00 2.57
2165 3245 4.393680 GCATAACGTTCCATTTCACCAGTA 59.606 41.667 2.82 0.00 0.00 2.74
2166 3246 3.190535 GCATAACGTTCCATTTCACCAGT 59.809 43.478 2.82 0.00 0.00 4.00
2179 3259 1.904287 TGGAGCAAAGGCATAACGTT 58.096 45.000 5.88 5.88 44.61 3.99
2185 3265 4.628963 AAAATTCTTGGAGCAAAGGCAT 57.371 36.364 0.00 0.00 44.61 4.40
2188 3268 5.473039 CCAGTAAAATTCTTGGAGCAAAGG 58.527 41.667 0.00 0.00 0.00 3.11
2226 3306 1.018752 TGATGCACCGTCACGAATGG 61.019 55.000 0.00 0.00 40.24 3.16
2260 5781 3.682155 CGTTATCACCCAACCCCGATTAA 60.682 47.826 0.00 0.00 0.00 1.40
2269 5790 2.172851 TGGACACGTTATCACCCAAC 57.827 50.000 0.00 0.00 0.00 3.77
2272 5793 2.073816 CACTTGGACACGTTATCACCC 58.926 52.381 0.00 0.00 0.00 4.61
2279 5800 1.416401 AGGTCATCACTTGGACACGTT 59.584 47.619 0.00 0.00 35.74 3.99
2306 5827 7.009907 GCCTACCTGTGTTAAACGTATAAGAAG 59.990 40.741 0.00 0.00 0.00 2.85
2311 5832 5.657826 TGCCTACCTGTGTTAAACGTATA 57.342 39.130 0.00 0.00 0.00 1.47
2431 5958 8.514330 AATAGCCGTTAGATTTTGGTAATTCA 57.486 30.769 0.00 0.00 0.00 2.57
2432 5959 9.797556 AAAATAGCCGTTAGATTTTGGTAATTC 57.202 29.630 0.00 0.00 32.83 2.17
2437 5964 9.984190 TTTTTAAAATAGCCGTTAGATTTTGGT 57.016 25.926 0.55 0.00 35.14 3.67
2461 5988 4.082136 TGGCGGCCGTTAGATTTTATTTTT 60.082 37.500 28.70 0.00 0.00 1.94
2462 5989 3.444388 TGGCGGCCGTTAGATTTTATTTT 59.556 39.130 28.70 0.00 0.00 1.82
2463 5990 3.018149 TGGCGGCCGTTAGATTTTATTT 58.982 40.909 28.70 0.00 0.00 1.40
2464 5991 2.645802 TGGCGGCCGTTAGATTTTATT 58.354 42.857 28.70 0.00 0.00 1.40
2465 5992 2.335316 TGGCGGCCGTTAGATTTTAT 57.665 45.000 28.70 0.00 0.00 1.40
2604 6131 1.997606 GACCCGGAACTTACAATGACG 59.002 52.381 0.73 0.00 0.00 4.35
2740 6267 8.735303 TGTTACCAACATTTTCATAATGAACG 57.265 30.769 0.00 0.00 34.51 3.95
2759 6286 0.743345 GGACTGGTGGCGATGTTACC 60.743 60.000 0.00 0.00 35.05 2.85
2760 6287 0.036765 TGGACTGGTGGCGATGTTAC 60.037 55.000 0.00 0.00 0.00 2.50
2772 6299 0.250124 TGTAAGCGTTGGTGGACTGG 60.250 55.000 0.00 0.00 0.00 4.00
2778 6309 0.673644 CTCCCCTGTAAGCGTTGGTG 60.674 60.000 0.00 0.00 0.00 4.17
2828 7413 2.531206 GGCTAGCTAGAACACGTCAAG 58.469 52.381 25.15 0.00 0.00 3.02
2877 7470 1.313091 GGAAAGAACCCATGCGACCC 61.313 60.000 0.00 0.00 0.00 4.46
2897 7490 0.818938 GAGTCCTTCCTCTTCCGACC 59.181 60.000 0.00 0.00 0.00 4.79
2916 7509 1.337823 ACATCTCTCGGTTCGGTTTGG 60.338 52.381 0.00 0.00 0.00 3.28
2917 7510 1.993370 GACATCTCTCGGTTCGGTTTG 59.007 52.381 0.00 0.00 0.00 2.93
2918 7511 1.616865 TGACATCTCTCGGTTCGGTTT 59.383 47.619 0.00 0.00 0.00 3.27
2919 7512 1.254026 TGACATCTCTCGGTTCGGTT 58.746 50.000 0.00 0.00 0.00 4.44
2920 7513 1.067776 GTTGACATCTCTCGGTTCGGT 60.068 52.381 0.00 0.00 0.00 4.69
2922 7515 1.260206 CGTTGACATCTCTCGGTTCG 58.740 55.000 0.00 0.00 0.00 3.95
2941 7535 0.511221 CGGGTGACATGTCGTTTCAC 59.489 55.000 20.54 12.95 39.18 3.18
2942 7536 0.601576 CCGGGTGACATGTCGTTTCA 60.602 55.000 20.54 0.40 0.00 2.69
2943 7537 0.601841 ACCGGGTGACATGTCGTTTC 60.602 55.000 20.54 10.67 0.00 2.78
2944 7538 0.601841 GACCGGGTGACATGTCGTTT 60.602 55.000 20.54 1.92 0.00 3.60
2945 7539 1.005394 GACCGGGTGACATGTCGTT 60.005 57.895 20.54 0.00 0.00 3.85
2946 7540 1.750341 TTGACCGGGTGACATGTCGT 61.750 55.000 20.54 11.79 35.75 4.34
2947 7541 0.601576 TTTGACCGGGTGACATGTCG 60.602 55.000 20.54 9.39 35.75 4.35
2949 7543 0.762418 TCTTTGACCGGGTGACATGT 59.238 50.000 3.30 0.00 0.00 3.21
2950 7544 1.442769 CTCTTTGACCGGGTGACATG 58.557 55.000 3.30 0.00 0.00 3.21
2951 7545 0.321653 GCTCTTTGACCGGGTGACAT 60.322 55.000 3.30 0.00 0.00 3.06
2953 7547 0.670854 GAGCTCTTTGACCGGGTGAC 60.671 60.000 3.30 0.00 0.00 3.67
2954 7548 1.118965 TGAGCTCTTTGACCGGGTGA 61.119 55.000 16.19 0.00 0.00 4.02
2955 7549 0.951040 GTGAGCTCTTTGACCGGGTG 60.951 60.000 16.19 0.00 0.00 4.61
2956 7550 1.371558 GTGAGCTCTTTGACCGGGT 59.628 57.895 16.19 0.00 0.00 5.28
2957 7551 0.250295 TTGTGAGCTCTTTGACCGGG 60.250 55.000 16.19 0.00 0.00 5.73
2958 7552 1.151668 CTTGTGAGCTCTTTGACCGG 58.848 55.000 16.19 0.00 0.00 5.28
2959 7553 0.514691 GCTTGTGAGCTCTTTGACCG 59.485 55.000 16.19 0.17 45.65 4.79
2978 7572 7.992180 AACATCTAGTTCTTTTGTTGCTTTG 57.008 32.000 0.00 0.00 34.74 2.77
3120 8651 2.665052 GGACAGTAACGTTTCGGCTTAG 59.335 50.000 5.91 0.00 0.00 2.18
3127 8658 1.774639 TGCTCGGACAGTAACGTTTC 58.225 50.000 5.91 0.04 0.00 2.78
3169 8700 2.034076 CAGTGACGCGCTTTGTTTAAC 58.966 47.619 5.73 0.00 0.00 2.01
3185 8724 3.425892 GCAGAAGCACTAAGATTGCAGTG 60.426 47.826 0.00 0.00 42.83 3.66
3207 8746 1.006832 CGCCGACCACATAGGAAAAG 58.993 55.000 0.00 0.00 41.22 2.27
3283 8827 7.874016 TCGATTAAGAGTTAGCAAAACTGGTAA 59.126 33.333 8.99 7.48 0.00 2.85
3286 8830 6.369065 AGTCGATTAAGAGTTAGCAAAACTGG 59.631 38.462 8.99 0.00 0.00 4.00
3287 8831 7.116376 TCAGTCGATTAAGAGTTAGCAAAACTG 59.884 37.037 8.99 0.00 0.00 3.16
3288 8832 7.152645 TCAGTCGATTAAGAGTTAGCAAAACT 58.847 34.615 4.31 4.31 0.00 2.66
3289 8833 7.328737 TCTCAGTCGATTAAGAGTTAGCAAAAC 59.671 37.037 0.00 0.00 0.00 2.43
3290 8834 7.328737 GTCTCAGTCGATTAAGAGTTAGCAAAA 59.671 37.037 0.00 0.00 0.00 2.44
3291 8835 6.807230 GTCTCAGTCGATTAAGAGTTAGCAAA 59.193 38.462 0.00 0.00 0.00 3.68
3294 8838 6.126568 AGTCTCAGTCGATTAAGAGTTAGC 57.873 41.667 0.00 0.00 0.00 3.09
3297 8841 6.750148 ACAAAGTCTCAGTCGATTAAGAGTT 58.250 36.000 0.00 0.00 33.84 3.01
3298 8842 6.334102 ACAAAGTCTCAGTCGATTAAGAGT 57.666 37.500 0.00 0.00 0.00 3.24
3304 8848 9.653287 TGAAATATAACAAAGTCTCAGTCGATT 57.347 29.630 0.00 0.00 0.00 3.34
3305 8849 9.307121 CTGAAATATAACAAAGTCTCAGTCGAT 57.693 33.333 0.00 0.00 0.00 3.59
3306 8850 8.304596 ACTGAAATATAACAAAGTCTCAGTCGA 58.695 33.333 0.00 0.00 38.22 4.20
3307 8851 8.467402 ACTGAAATATAACAAAGTCTCAGTCG 57.533 34.615 0.00 0.00 38.22 4.18
3309 8853 8.304596 TCGACTGAAATATAACAAAGTCTCAGT 58.695 33.333 1.25 1.25 43.63 3.41
3310 8854 8.689251 TCGACTGAAATATAACAAAGTCTCAG 57.311 34.615 0.00 0.00 36.09 3.35
3311 8855 9.087424 CATCGACTGAAATATAACAAAGTCTCA 57.913 33.333 0.00 0.00 33.49 3.27
3312 8856 8.058915 GCATCGACTGAAATATAACAAAGTCTC 58.941 37.037 0.00 0.00 33.49 3.36
3314 8858 7.910304 AGCATCGACTGAAATATAACAAAGTC 58.090 34.615 0.00 0.00 0.00 3.01
3315 8859 7.849804 AGCATCGACTGAAATATAACAAAGT 57.150 32.000 0.00 0.00 0.00 2.66
3331 8875 9.535270 GCAAGATTAAAGAAATATAGCATCGAC 57.465 33.333 0.00 0.00 0.00 4.20
3332 8876 9.271828 TGCAAGATTAAAGAAATATAGCATCGA 57.728 29.630 0.00 0.00 0.00 3.59
3344 8888 6.599244 ACGAATCTCCATGCAAGATTAAAGAA 59.401 34.615 16.94 0.00 42.17 2.52
3345 8889 6.115446 ACGAATCTCCATGCAAGATTAAAGA 58.885 36.000 16.94 0.00 42.17 2.52
3346 8890 6.369059 ACGAATCTCCATGCAAGATTAAAG 57.631 37.500 16.94 14.21 42.17 1.85
3347 8891 6.821160 TGTACGAATCTCCATGCAAGATTAAA 59.179 34.615 16.94 7.16 42.17 1.52
3348 8892 6.257849 GTGTACGAATCTCCATGCAAGATTAA 59.742 38.462 16.94 7.41 42.17 1.40
3349 8893 5.753438 GTGTACGAATCTCCATGCAAGATTA 59.247 40.000 16.94 4.57 42.17 1.75
3350 8894 4.572389 GTGTACGAATCTCCATGCAAGATT 59.428 41.667 16.94 16.94 44.21 2.40
3351 8895 4.122776 GTGTACGAATCTCCATGCAAGAT 58.877 43.478 0.00 0.00 34.96 2.40
3352 8896 3.056179 TGTGTACGAATCTCCATGCAAGA 60.056 43.478 0.00 0.00 0.00 3.02
3353 8897 3.261580 TGTGTACGAATCTCCATGCAAG 58.738 45.455 0.00 0.00 0.00 4.01
3354 8898 3.326836 TGTGTACGAATCTCCATGCAA 57.673 42.857 0.00 0.00 0.00 4.08
3355 8899 3.326836 TTGTGTACGAATCTCCATGCA 57.673 42.857 0.00 0.00 0.00 3.96
3358 8902 7.687941 AGAAAATTTGTGTACGAATCTCCAT 57.312 32.000 0.00 0.00 0.00 3.41
3359 8903 7.504924 AAGAAAATTTGTGTACGAATCTCCA 57.495 32.000 0.00 0.00 0.00 3.86
3360 8904 8.073768 TGAAAGAAAATTTGTGTACGAATCTCC 58.926 33.333 0.00 0.00 0.00 3.71
3362 8906 8.621286 ACTGAAAGAAAATTTGTGTACGAATCT 58.379 29.630 0.00 0.00 37.43 2.40
3363 8907 8.782533 ACTGAAAGAAAATTTGTGTACGAATC 57.217 30.769 0.00 0.00 37.43 2.52
3367 10308 8.643752 ACAAAACTGAAAGAAAATTTGTGTACG 58.356 29.630 0.00 0.00 37.99 3.67
3385 10326 7.600375 TCAGCTAGATGAGTTCTAACAAAACTG 59.400 37.037 6.59 0.00 37.10 3.16
3386 10327 7.671302 TCAGCTAGATGAGTTCTAACAAAACT 58.329 34.615 6.59 0.00 39.61 2.66
3387 10328 7.891183 TCAGCTAGATGAGTTCTAACAAAAC 57.109 36.000 6.59 0.00 36.50 2.43
3400 10341 8.972127 AGACATAACTAAAACTCAGCTAGATGA 58.028 33.333 10.81 10.81 0.00 2.92
3401 10342 9.243637 GAGACATAACTAAAACTCAGCTAGATG 57.756 37.037 0.24 0.24 0.00 2.90
3402 10343 8.972127 TGAGACATAACTAAAACTCAGCTAGAT 58.028 33.333 0.00 0.00 32.04 1.98
3403 10344 8.349568 TGAGACATAACTAAAACTCAGCTAGA 57.650 34.615 0.00 0.00 32.04 2.43
3404 10345 9.593134 AATGAGACATAACTAAAACTCAGCTAG 57.407 33.333 0.00 0.00 37.70 3.42
3405 10346 9.587772 GAATGAGACATAACTAAAACTCAGCTA 57.412 33.333 0.00 0.00 37.70 3.32
3406 10347 8.097038 TGAATGAGACATAACTAAAACTCAGCT 58.903 33.333 0.00 0.00 37.70 4.24
3407 10348 8.171840 GTGAATGAGACATAACTAAAACTCAGC 58.828 37.037 0.00 0.00 37.70 4.26
3417 10358 9.331282 GGCTATAAAAGTGAATGAGACATAACT 57.669 33.333 0.00 0.00 0.00 2.24
3418 10359 9.109393 TGGCTATAAAAGTGAATGAGACATAAC 57.891 33.333 0.00 0.00 0.00 1.89
3422 10363 7.067372 CCAATGGCTATAAAAGTGAATGAGACA 59.933 37.037 0.00 0.00 0.00 3.41
3423 10364 7.283127 TCCAATGGCTATAAAAGTGAATGAGAC 59.717 37.037 0.00 0.00 0.00 3.36
3425 10366 7.572523 TCCAATGGCTATAAAAGTGAATGAG 57.427 36.000 0.00 0.00 0.00 2.90
3427 10368 7.650504 CACATCCAATGGCTATAAAAGTGAATG 59.349 37.037 0.00 0.00 33.60 2.67
3429 10370 6.889177 TCACATCCAATGGCTATAAAAGTGAA 59.111 34.615 0.00 0.00 33.60 3.18
3430 10371 6.422333 TCACATCCAATGGCTATAAAAGTGA 58.578 36.000 0.00 0.00 33.60 3.41
3431 10372 6.698008 TCACATCCAATGGCTATAAAAGTG 57.302 37.500 0.00 0.00 33.60 3.16
3432 10373 6.239120 GCATCACATCCAATGGCTATAAAAGT 60.239 38.462 0.00 0.00 33.60 2.66
3433 10374 6.015688 AGCATCACATCCAATGGCTATAAAAG 60.016 38.462 0.00 0.00 33.60 2.27
3436 10377 4.989277 AGCATCACATCCAATGGCTATAA 58.011 39.130 0.00 0.00 33.60 0.98
3437 10378 4.645863 AGCATCACATCCAATGGCTATA 57.354 40.909 0.00 0.00 33.60 1.31
3439 10380 4.645863 ATAGCATCACATCCAATGGCTA 57.354 40.909 0.00 0.00 33.60 3.93
3441 10382 5.005740 TCTTATAGCATCACATCCAATGGC 58.994 41.667 0.00 0.00 33.60 4.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.